Spectral analysis of protein sequences

Analysis of protein sequences can avoid many problems inherently existing in the study of nucleotide sequences given the knowledge that DNA sequences contain all the information for regulating protein expression. This paper presents a spectral approach for calculating the similarity of protein sequences, which can be useful for the inferences of protein functions. The proposed method is based on the mathematical concepts of linear predictive coding and cepstral distortion measure. We show that this spectral approach can reveal non-trivial results from an experimental study of a set of functionally related and functionally non-related protein sequences, and has advantages over some existing approaches

ABSTRACT Wang, Zhi. Spectral Analysis of Protein Sequences. (Under the direction of Dr.

The purpose of this research is to elucidate how to apply spectral analysis methods to understand the structure, function and evolution of protein sequences. In the first part of this research, spectral analyses have been applied to the basic-helix-loop-helix (bHLH) family of transcription factors. It is shown that the periodicity of the bHLH variability pattern (entropy profile) conforms to the classical α-helix periodicity of 3.6 amino acids per turn. Further, the underlying physiochemical attributes profiles (factor score profiles) are examined and their periodicities also have significant implications of the α-helix secondary structure. It is suggested that the entropy profile can be well explained by the five factor score variance components that reflect the polarity/hydrophobicity, secondary structure information, molecular volume, codon composition and electrostatic charge attributes of amino acids. In the second part of this research, complex demodulation (CDM) method is introduced in an attempt to quantify the amplitude of periodic components in protein sequences. Proteins are often considered to be “multiple domain entities ” because they are composed of a number of functionally and structurally distinct domains with potentially independent origins. The analyses of bZIP and bHLH-PAS protein domains found that complex demodulation procedures can provide important insight about functional and structural attributes. It is found that the local amplitude minimums or maximums are associated with the boundary between two structural or functional components. In the third part of this research, the periodicity evaluation of a leucine zipper protein domain with a well-known structure is used to rank 494 published indices summarized in a databas